Alexander Grueneberg agrueneberg

## tcga-file-search.postman_collection
{
	"id": "4f972238-9569-c553-f31b-d13f05a7af9f",
	"name": "TCGA File Search API",
	"description": "See https://tcga-data.nci.nih.gov/ccg-data-web/search.jsp?projectId=1",
	"order": [
		"16f2ef6f-8874-22b6-c702-ff6fc98b31e3",
		"a3821414-552b-37e4-8123-b2d8cfd92216",
		"1965c0e3-1217-717f-3f2a-b48f24cb7043",
		"805128a2-7729-90dd-4ff6-ae9af4a5a633",
		"9710c160-0f7e-06a9-695b-2a5601f60404",

## parallel.R
library(parallel)
library(BGLR)
library(microbenchmark)

data(mice)
X <- mice.X
y <- mice.pheno$Obesity.BMI

GWAS <- function (i) {
  summary(lm(y ~ X[, i]))$coef[2, ]

## query.sparql
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX tcga:<http://purl.org/tcga/core#>
PREFIX tcgameta:<http://purl.org/tcga/metadata#>
PREFIX tcgaclin:<http://purl.org/tcga/clin#>
PREFIX tcgaclinProp:<http://purl.org/tcga/clin#property/>
SELECT ?patientId ?tumorTissueSite ?ageAtInitialDiagnosis ?gender ?race ?vitalStatus
WHERE {
  SERVICE <http://agalpha.mathbiol.org:10035/repositories/tcga> {
    ?file tcga:platform ?platform .
    ?platform rdfs:label "mda_rppa_core" .

## TCGA.R
library(RCurl)
library(rjson)

TCGA.get <- function (uri) {
    getURI(uri)
}

TCGA.find <- function (query) {
    uri <- paste("http://agalpha.mathbiol.org/repositories/tcga?infer=true&query=", URLencode(query, reserved=TRUE), sep="")
    response <- fromJSON(getURI(uri, httpheader=c("Accept: application/sparql-results+json")))

## gist:4157870

      
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                agrueneberg
                / gist:4157870
            
            
              Created
              November 27, 2012 23:12
            
              
                @ControllerAdvice in Spring MVC 3.2
              
          
    Spring MVC 3.2 introduces the @ControllerAdvice component annotation that allows you define single @ExceptionHandler methods for all your controllers.
If you find yourself that the exception handlers are not working the way they are supposed to and you happen to have a clearly separated root and web scope, make sure that that you are including the @ControllerAdvice component in the web scope rather than the root scope, i.e. include org.springframework.web.bind.annotation.ControllerAdvice in context:component-scan:
<context:component-scan base-package="[path]" use-default-filters="false">
  <context:include-filter expression="org.springframework.stereotype.Controller" type="annotation" />
  <context:include-filter expression="org.springframework.web.bind.annotation.ControllerAdvice" type="annotation" />


## push-docs.sh
#!/bin/bash
set -e
# Only run on normal commits, ignore pull requests
if [ "${TRAVIS_PULL_REQUEST}" = "false" ]; then
    # Clone gh-pages branch into inst/web
    git clone --branch gh-pages https://${GH_TOKEN}@github.com/${TRAVIS_REPO_SLUG}.git inst/web
    # Copy README
    cp README.md inst/web
    # Run staticdocs
    Rscript -e 'library(staticdocs); library(methods); build_site(launch = FALSE)'

## gist:3842413
library(RCurl)
library(rjson)

# Read sample UUIDs.
uuids <- read.csv(file="~/uuids.csv")

# Convert to character vector.
uuids <- as.vector(t(uuids))

# Query TCGA's UUID to barcode Web Service.

## ufw-syncthing
[Syncthing]
title=Syncthing
description=Open Source Continuous File Synchronization
ports=22000/tcp|21025/udp

## generate-random-matrix.c
#include <errno.h>
#include <fcntl.h>
#include <stdio.h>
#include <stdlib.h>
#include <time.h>

int main(int argc, char **argv) {
 // Get arguments
    if (argc != 4) {
        fprintf(stderr, "usage: %s nrows ncols filename\n", argv[0]);

## client.html
<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <title>HMAC-SHA256 Example</title>
</head>
<body>
    <script src="http://crypto.stanford.edu/sjcl/sjcl.js"></script>
    <script>
        var sharedSecret, query, signature, hmac, xhr;
	{
	"id": "4f972238-9569-c553-f31b-d13f05a7af9f",
	"name": "TCGA File Search API",
	"description": "See https://tcga-data.nci.nih.gov/ccg-data-web/search.jsp?projectId=1",
	"order": [
	"16f2ef6f-8874-22b6-c702-ff6fc98b31e3",
	"a3821414-552b-37e4-8123-b2d8cfd92216",
	"1965c0e3-1217-717f-3f2a-b48f24cb7043",
	"805128a2-7729-90dd-4ff6-ae9af4a5a633",
	"9710c160-0f7e-06a9-695b-2a5601f60404",
	library(parallel)
	library(BGLR)
	library(microbenchmark)

	data(mice)
	X <- mice.X
	y <- mice.pheno$Obesity.BMI

	GWAS <- function (i) {
	summary(lm(y ~ X[, i]))$coef[2, ]
	PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
	PREFIX tcga:<http://purl.org/tcga/core#>
	PREFIX tcgameta:<http://purl.org/tcga/metadata#>
	PREFIX tcgaclin:<http://purl.org/tcga/clin#>
	PREFIX tcgaclinProp:<http://purl.org/tcga/clin#property/>
	SELECT ?patientId ?tumorTissueSite ?ageAtInitialDiagnosis ?gender ?race ?vitalStatus
	WHERE {
	SERVICE <http://agalpha.mathbiol.org:10035/repositories/tcga> {
	?file tcga:platform ?platform .
	?platform rdfs:label "mda_rppa_core" .
	library(RCurl)
	library(rjson)

	TCGA.get <- function (uri) {
	getURI(uri)
	}

	TCGA.find <- function (query) {
	uri <- paste("http://agalpha.mathbiol.org/repositories/tcga?infer=true&query=", URLencode(query, reserved=TRUE), sep="")
	response <- fromJSON(getURI(uri, httpheader=c("Accept: application/sparql-results+json")))
	#!/bin/bash
	set -e
	# Only run on normal commits, ignore pull requests
	if [ "${TRAVIS_PULL_REQUEST}" = "false" ]; then
	# Clone gh-pages branch into inst/web
	git clone --branch gh-pages https://${GH_TOKEN}@github.com/${TRAVIS_REPO_SLUG}.git inst/web
	# Copy README
	cp README.md inst/web
	# Run staticdocs
	Rscript -e 'library(staticdocs); library(methods); build_site(launch = FALSE)'
	library(RCurl)
	library(rjson)

	# Read sample UUIDs.
	uuids <- read.csv(file="~/uuids.csv")

	# Convert to character vector.
	uuids <- as.vector(t(uuids))

	# Query TCGA's UUID to barcode Web Service.
	[Syncthing]
	title=Syncthing
	description=Open Source Continuous File Synchronization
	ports=22000/tcp\|21025/udp
	#include <errno.h>
	#include <fcntl.h>
	#include <stdio.h>
	#include <stdlib.h>
	#include <time.h>

	int main(int argc, char **argv) {
	// Get arguments
	if (argc != 4) {
	fprintf(stderr, "usage: %s nrows ncols filename\n", argv[0]);
	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<title>HMAC-SHA256 Example</title>
	</head>
	<body>
	<script src="http://crypto.stanford.edu/sjcl/sjcl.js"></script>
	<script>
	var sharedSecret, query, signature, hmac, xhr;